Data from: Geomolecular dating and the origin of placental mammals

In modern evolutionary divergence analysis the role of geological information extends beyond providing a timescale, to informing molecular rate variation across the tree. Here I consider the implications of this development. I use fossil calibrations to test the accuracy of models of molecular rate evolution for placental mammals, and reveal substantial misspecification associated with life history rate correlates. Adding further calibrations to reduce dating errors at specific nodes unfortunately tends to transfer underlying rate errors to adjacent branches. Thus, tight calibration across the tree is vital to buffer against rate model errors. I argue that this must include allowing maximum bounds to be tight when good fossil records permit, otherwise divergences deep in the tree will tend to be inflated by the interaction of rate errors and asymmetric confidence in minimum and maximum bounds. In the case of placental mammals I sought to reduce the potential for transferring calibration and rate model errors across the tree by focusing on well-supported calibrations with appropriately conservative maximum bounds. The resulting divergence estimates are younger than others published recently, and provide the long-anticipated molecular signature for the placental mammal radiation observed in the fossil record near the 66 Ma Cretaceous-Paleogene extinction event.

在现代演化分化分析中，地质信息的作用已不再局限于提供时间标尺，而是可用于揭示系统发育树各分支的分子速率变异规律。本文就此发展趋势的研究意义展开探讨。本文以胎盘类哺乳动物（placental mammals）为研究对象，利用化石校准（fossil calibration）测试其分子速率演化模型的准确性，并揭示出与生命史速率相关因素显著的模型设定偏误。然而，为减少特定演化节点的定年误差而增加更多校准点，往往会将潜在的速率误差转移至相邻分支。因此，对整个系统发育树实施严格的校准，是抵消速率模型误差的关键手段。本文认为，这一手段需包含：当具备充分的化石记录时，应设置严格的最大年代约束；否则，演化树深处的分化时间估计值，会因速率误差与最小、最大年代约束间非对称置信度的相互作用而被高估。针对胎盘类哺乳动物的研究中，本文通过聚焦于得到充分支持的校准点，并设置恰当保守的最大年代约束，以降低校准误差与速率模型误差在系统发育树中扩散的可能性。本次研究得到的分化时间估计值较近期发表的其他结果更年轻，同时为化石记录中于66 Ma白垩纪-古近纪灭绝事件附近观测到的胎盘类哺乳动物演化辐射，提供了期待已久的分子生物学佐证。